When I get new boots, I try them on and size them for the conditions I will be fishing the most. For me, most of the time will be during warmer (above freezing) conditions so I typically buy boots that will work for waders and 1 pair of normal socks.

They are a bit snug during the winter when I have a thicker pair of wool socks on, but it's nothing a little loosening of the laces can't fix.

I think if I had a similar problem to yours, I might consider taking an old pair of waders that I no longer use, cutting the neoprene booties off, and doubling up. This should tighten up your boots